The site was founded in the Bronze Age as Ithome, an ancient city originally of Achaean Greeks which eventually came under the hegemony of Sparta. Many inhabitants went into exile, and eventually it was destroyed by the Spartans and abandoned for some time.

After the defeat of the Spartans at the Battle of Leuctra the Theban general Epaminondas recalled the Messenians who had fled Spartan rule and in 369 BC founded Messene with them as the capital of the new state of Messenia. Messene retained some importance even during the Roman imperial period and was never destroyed or completely buried by later settlements. The remains of a basilica attest to a settlement even in the early Byzantine era.

The site is surrounded by a nine-kilometer-long fortification wall. At the heart of the social and economic life was the massive Agora. It was surrounded by colonnaded stoas. The city also boasts a stadium and an adjoining gymnasium for athletic training.

Excavations and reconstructions have been carried out at this archaeological site for decades, yet around 65 per cent of the site remains unexcavated